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To analyze the clinical characteristics and genotype of a patient with congenital systemic lipodystrophy (CGL) type 1 associated with exudative xanthoma caused by AGPAT2 gene mutation, and to provide evidence for clinical and genetic diagnosis of the disease. Methods Clinical data of the patient such as medical history, physical examination and laboratory examination were collected. Peripheral venous blood was collected for whole exome sequencing analysis and Sanger sequencing verification, and treatment was provided to patients according to the changes of condition. Results The clinical manifestations of the patient were subcutaneous fat reduction, fatty liver, spleen enlargement, kidney enlargement, high blood sugar and lipids, severe insulin resistance, scattered yellow rash on limbs, which was confirmed as xanthoma. The results of whole exon sequencing showed that the AGPAT2 gene of the patient had a heterozygous nonsense mutation of c. 202C>T:p. R68 and c. 646A>T:p. K216, and the former was the pathogenic mutation site. Follow-up therapy covers improvement of lifestyle, low-fat diet and regular exercise. The rashes subsided after active lipid-lowering therapy. Conclusions Apart from typical lipodystrophy, the patient was accompanied by exanthemous xanthoma. No CGLI patient with exanthemous xanthoma has been reported in the domestic literature database up to now, and the genetic test results showed that there was a c. 202C>T heterozygous mutation of AGPAT2 gene. This gene site has not been reported in the literature, and its functional verification needs to be further studied. [ABSTRACT FROM AUTHOR]